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Article
Open AccessDeepGRP: engineering a software tool for predicting genomic repetitive elements using Recurrent Neural Networks with attention
Repetitive elements contribute a large part of eukaryotic genomes. For example, about 40 to 50% of human, mouse and rat genomes are repetitive. So identifying and classifying repeats is an important step in ge...
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Article
Open AccessHydrothermal chimneys host habitat-specific microbial communities: analogues for studying the possible impact of mining seafloor massive sulfide deposits
To assess the risk that mining of seafloor massive sulfides (SMS) from extinct hydrothermal vent environments has for changing the ecosystem irreversibly, we sampled SMS analogous habitats from the Kairei and ...
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Article
Endemic hydrothermal vent species identified in the open ocean seed bank
Hydrothermal vent systems host microbial communities among which several microorganisms have been considered endemic to this type of habitat. It is still unclear how these organisms colonize geographically dis...
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Article
Open AccessFISH Oracle 2: a web server for integrative visualization of genomic data in cancer research
A comprehensive view on all relevant genomic data is instrumental for understanding the complex patterns of molecular alterations typically found in cancer cells. One of the most effective ways to rapidly obta...
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Article
Open AccessFast online and index-based algorithms for approximate search of RNA sequence-structure patterns
It is well known that the search for homologous RNAs is more effective if both sequence and structure information is incorporated into the search. However, current tools for searching with RNA sequence-structu...
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Article
Open AccessLTRsift: a graphical user interface for semi-automatic classification and postprocessing of de novo detected LTR retrotransposons
Long terminal repeat (LTR) retrotransposons are a class of eukaryotic mobile elements characterized by a distinctive sequence similarity-based structure. Hence they are well suited for computational identifica...
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Article
Open AccessReadjoiner: a fast and memory efficient string graph-based sequence assembler
Ongoing improvements in throughput of the next-generation sequencing technologies challenge the current generation of de novo sequence assemblers. Most recent sequence assemblers are based on the construction ...
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Article
Open AccessFISH Oracle: a web server for flexible visualization of DNA copy number data in a genomic context
The rapidly growing amount of array CGH data requires improved visualization software supporting the process of identifying candidate cancer genes. Optimally, such software should work across multiple microarr...
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Article
Open AccessStructator: fast index-based search for RNA sequence-structure patterns
The secondary structure of RNA molecules is intimately related to their function and often more conserved than the sequence. Hence, the important task of searching databases for RNAs requires to match sequence...
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Article
Open AccessSequencing, annotation, and comparative genome analysis of the gerbil-adapted Helicobacter pylori strain B8
The Mongolian gerbils are a good model to mimic the Helicobacter pylori-associated pathogenesis of the human stomach. In the current study the gerbil-adapted strain B8 was completely sequenced, annotated and comp...
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Article
Open AccessSelective regain of egfr gene copies in CD44+/CD24-/lowbreast cancer cellular model MDA-MB-468
Increased transcription of oncogenes like the epidermal growth factor receptor (EGFR) is frequently caused by amplification of the whole gene or at least of regulatory sequences. Aim of this study was to pinpo...
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MetaGenomeThreader: A Software Tool for Predicting Genes in DNA-Sequences of Metagenome Projects
We consider a gene finding method that is specifically designed to work on metagenome sequences. The method can handle short metagenome sequences with in-frame stop codons as well as frame shifts. It delivers ...
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Article
Open AccessCoCoNUT: an efficient system for the comparison and analysis of genomes
Comparative genomics is the analysis and comparison of genomes from different species. This area of research is driven by the large number of sequenced genomes and heavily relies on efficient algorithms and so...
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Article
Open AccessA new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes
The challenges of accurate gene prediction and enumeration are further aggravated in large genomes that contain highly repetitive transposable elements (TEs). Yet TEs play a substantial role in genome evolutio...
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Article
Open AccessEfficient computation of absent words in genomic sequences
Analysis of sequence composition is a routine task in genome research. Organisms are characterized by their base composition, dinucleotide relative abundance, codon usage, and so on. Unique subsequences are ma...
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Article
Open AccessLTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons
Transposable elements are abundant in eukaryotic genomes and it is believed that they have a significant impact on the evolution of gene and chromosome structure. While there are several completed eukaryotic g...
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Article
Open AccessOptimising oligonucleotide array design for ChIP-on-chip
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Visualization of Syntenic Relationships With SynBrowse
Synteny is the preserved order of genes between related species. To detect syntenic regions one usually first applies sequence comparison methods to the genomic sequences of the considered species. Sequence si...
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Article
Open AccessFast index based algorithms and software for matching position specific scoring matrices
In biological sequence analysis, position specific scoring matrices (PSSMs) are widely used to represent sequence motifs in nucleotide as well as amino acid sequences. Searching with PSSMs in complete genomes ...
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Chapter
A Computational Approach to Search for Non-Coding RNAs in Large Genomic Data
Over the last few years several specialized software tools have been developed, each allowing a certain class of RNAs insequencedatatobe found.Herewedescribeageneral tool that allows us to specify many differe...